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FastaFromBam tool help

FastaFromBam (2024_08-113-g94a3b440)

Download the reference genome FASTA file for a BAM/CRAM file.

Mandatory parameters:
  -in <file>        Input BAM/CRAM file.
  -out <file>       Output reference genome FASTA file.

Optional parameters:
  -ref <file>       Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                    Default value: ''

Special parameters:
  --help            Shows this help and exits.
  --version         Prints version and exits.
  --changelog       Prints changeloge and exits.
  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
  --settings [file] Settings override file (no other settings files are used).

FastaFromBam changelog

FastaFromBam 2024_08-113-g94a3b440

2024-08-18 Initial version.

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